Input and runtime details for job 5882223 (precomputed example)

Sequence input

	sRNA sequences		[.fa]
	Putative target sequences (organism of interest)		[.fa]
	Extract sequences around		start codon
	nt up (1-300)		200
	nt down (1-300)		100

CopraRNA parameters

	Consensus prediction		off
	p-value combination		no
	p-value filtering (0=off)		0

IntaRNA parameters

	Target folding window size		150
	Target max. basepair distance		100

Job ID 5882223 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:29:59 CET 2018
	CopraRNA Started		@ Fri Feb 16 20:39:56 CET 2018
	CopraRNA Finished & Post-Processing		@ Sat Feb 17 03:02:39 CET 2018
	Post-Processing Finished		@ Sat Feb 17 03:02:47 CET 2018
	Job Completed		@ Sat Feb 17 03:03:15 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=5882223&toolName=CopraRNA ( 30 days expiry )

Description of the job

Spot42

Output download complete results [zip]

Downloadable files

	CopraRNA result table:		[csv]
	Functional enrichment file		[txt]
	Auxiliary enrichment file		[csv]
	mRNA regions plot		[png] [pdf] [ps]
	sRNA regions plot		[png] [pdf] [ps]
	Functional annotation chart		[html] [pdf]
	Phylogenetic conservation		[png] [pdf]
	16S rDNA tree		[txt] [svg]

mRNA region plot

sRNA region plot

Annot. chart

Conserved, identified interactions for NC_000913 Escherichia coli str. K-12 substr. MG1655

Select: 1-10 11-20 21-30 31-40 41-50 51-60 61-70 71-80 81-90 91-100 101-110 111-120 121-130 131-140 141-150 151-160 161-170 171-180 181-190 191-200 all

Sort by selecting a column name:

Rank	CopraRNA p-value	CopraRNA fdr value	Locus Tag	Gene Name	Energy [kcal/mol]	IntaRNA p-value	Position mRNA	Position sRNA	Annotation
173	0.007216	0.1466	b3650	spoT	-5.39	0.520602	11 -- 17	54 -- 60	bifunctional (p)ppGpp synthetase II/ guanosine-3' 5'-bis pyrophosphate 3'-pyrophosphohydrolase	_____________10______18\n_____________\|_______\|\n5'-UAG...GGAAA_______CUGGU...CUC-3'\n______________GGAUCCG\n______________::\|\|\|\|\|\n______________UUUAGGC\n3'-AUU...GUCGG_______UAAUG...AUG-5'\n_____________\|_______\|\n_____________61______53\n	11 -- 17	54 -- 60	-6.87427 kcal/mol	1.21245 kcal/mol	0.286889 kcal/mol	10 18@LB@ \| \|@LB@5'-UAG...GGAAA CUGGU...CUC-3'@LB@ GGAUCCG@LB@ ::\|\|\|\|\|@LB@ UUUAGGC@LB@3'-AUU...GUCGG UAAUG...AUG-5'@LB@ \| \|@LB@ 61 53@LB@@LB@@LB@Energy -5.39 kcal/mol@LB@Hybridization Energy -6.87427 kcal/mol@LB@Unfolding Energy - mRNA 1.21245 kcal/mol@LB@Unfolding Energy - sRNA 0.286889 kcal/mol@LB@@LB@Position - mRNA 11 -- 17@LB@Position - sRNA 54 -- 60@LB@Position Seed - mRNA 11 -- 17@LB@Position Seed - sRNA 54 -- 60@LB@
147	0.005606	0.1342	b3085	ygjP	-7.80	0.173342	13 -- 33	55 -- 72	putative metal dependent hydrolase	_____________12____________________34\n_____________\|_____________________\|\n5'-AAC...GCAGC_________UCC____CU___CACGC...AAC-3'\n______________AAAUAUUCA___GCCG__UCC\n______________\|\|\|\|\|\|\|\|\|___\|\|\|:__\|\|\|\n______________UUUAUAAGU___CGGU__AGG\n3'-AUU...CCGAU________________UU___CUAAU...AUG-5'\n_____________\|_____________________\|\n_____________73____________________54\n	14 -- 20	65 -- 71	-15.2572 kcal/mol	1.39359 kcal/mol	6.08601 kcal/mol	12 34@LB@ \| \|@LB@5'-AAC...GCAGC UCC CU CACGC...AAC-3'@LB@ AAAUAUUCA GCCG UCC@LB@ \|\|\|\|\|\|\|\|\| \|\|\|: \|\|\|@LB@ UUUAUAAGU CGGU AGG@LB@3'-AUU...CCGAU UU CUAAU...AUG-5'@LB@ \| \|@LB@ 73 54@LB@@LB@@LB@Energy -7.80 kcal/mol@LB@Hybridization Energy -15.2572 kcal/mol@LB@Unfolding Energy - mRNA 1.39359 kcal/mol@LB@Unfolding Energy - sRNA 6.08601 kcal/mol@LB@@LB@Position - mRNA 13 -- 33@LB@Position - sRNA 55 -- 72@LB@Position Seed - mRNA 14 -- 20@LB@Position Seed - sRNA 65 -- 71@LB@
60	0.0009057	0.0531	b2740	ygbN	-7.72	0.181404	16 -- 72	3 -- 58	putative transporter	_____________15__________________________________________________________73\n_____________\|___________________________________________________________\|\n5'-GUG...CGCCU_______G_G_____A__UC___G_____UC___UGU______AA__________G___CACCG...UCC-3'\n______________GUUCGAU_A_GUGGG_UA__AGG_CUGGA__GGU___GAAUAU___ACCUC_GUG_CCU\n______________:\|:\|\|\|\|_\|_\|\|\|::_\|\|__\|\|\|_\|\|\|:\|__\|:\|___\|\|\|:\|\|___\|\|\|\|\|_\|\|:_\|\|\|\n______________UAGGCUA_U_CACUU_AU__UCC_GACUU__CUA___CUUGUA___UGGAG_CAU_GGA\n3'-AUU...CGGUU_______A_G_____C__UU___A_____U____U________GAA_____A___G___UG-5'\n_____________\|___________________________________________________________\|\n_____________59__________________________________________________________2\n	16 -- 22	52 -- 58	-40.891 kcal/mol	20.495 kcal/mol	12.7026 kcal/mol	15 73@LB@ \| \|@LB@5'-GUG...CGCCU G G A UC G UC UGU AA G CACCG...UCC-3'@LB@ GUUCGAU A GUGGG UA AGG CUGGA GGU GAAUAU ACCUC GUG CCU@LB@ :\|:\|\|\|\| \| \|\|\|:: \|\| \|\|\| \|\|\|:\| \|:\| \|\|\|:\|\| \|\|\|\|\| \|\|: \|\|\|@LB@ UAGGCUA U CACUU AU UCC GACUU CUA CUUGUA UGGAG CAU GGA@LB@3'-AUU...CGGUU A G C UU A U U GAA A G UG-5'@LB@ \| \|@LB@ 59 2@LB@@LB@@LB@Energy -7.72 kcal/mol@LB@Hybridization Energy -40.891 kcal/mol@LB@Unfolding Energy - mRNA 20.495 kcal/mol@LB@Unfolding Energy - sRNA 12.7026 kcal/mol@LB@@LB@Position - mRNA 16 -- 72@LB@Position - sRNA 3 -- 58@LB@Position Seed - mRNA 16 -- 22@LB@Position Seed - sRNA 52 -- 58@LB@
186	0.008252	0.1556	b2026	hisI	-8.65	0.106637	17 -- 26	42 -- 51	phosphoribosyl-AMP cyclohydrolase and phosphoribosyl-ATP pyrophosphatase	_____________16_________27\n_____________\|__________\|\n5'-GAA...AAAAG__________UUGCC...UGC-3'\n______________UGCGUGAAGU\n______________\|:\|\|\|\|\|\|\|\|\n______________AUGCACUUCA\n3'-AUU...GGCUA__________UUUUC...AUG-5'\n_____________\|__________\|\n_____________52_________41\n	20 -- 26	42 -- 48	-13.8545 kcal/mol	1.95631 kcal/mol	3.26026 kcal/mol	16 27@LB@ \| \|@LB@5'-GAA...AAAAG UUGCC...UGC-3'@LB@ UGCGUGAAGU@LB@ \|:\|\|\|\|\|\|\|\|@LB@ AUGCACUUCA@LB@3'-AUU...GGCUA UUUUC...AUG-5'@LB@ \| \|@LB@ 52 41@LB@@LB@@LB@Energy -8.65 kcal/mol@LB@Hybridization Energy -13.8545 kcal/mol@LB@Unfolding Energy - mRNA 1.95631 kcal/mol@LB@Unfolding Energy - sRNA 3.26026 kcal/mol@LB@@LB@Position - mRNA 17 -- 26@LB@Position - sRNA 42 -- 51@LB@Position Seed - mRNA 20 -- 26@LB@Position Seed - sRNA 42 -- 48@LB@
194	0.008663	0.1558	b0213	yafS	-5.39	0.521143	17 -- 34	51 -- 73	putative S-adenosyl-L-methionine-dependent methyltransferase	_____________16______________________35\n_____________\|_______________________\|\n5'-UGG...GGUGA_______________________GCCAG...UCA-3'\n______________GAAAUAU__GGCC___UCCGGUU\n______________:\|\|\|\|\|\|__:\|\|\|___\|\|\|\|:\|\|\n______________UUUUAUA__UCGG___AGGCUAA\n3'-AUU...GCCGA_______AG____UUU_______UGCAC...AUG-5'\n_____________\|_______________________\|\n_____________74______________________50\n	28 -- 34	51 -- 57	-15.2768 kcal/mol	3.69768 kcal/mol	6.213 kcal/mol	16 35@LB@ \| \|@LB@5'-UGG...GGUGA GCCAG...UCA-3'@LB@ GAAAUAU GGCC UCCGGUU@LB@ :\|\|\|\|\|\| :\|\|\| \|\|\|\|:\|\|@LB@ UUUUAUA UCGG AGGCUAA@LB@3'-AUU...GCCGA AG UUU UGCAC...AUG-5'@LB@ \| \|@LB@ 74 50@LB@@LB@@LB@Energy -5.39 kcal/mol@LB@Hybridization Energy -15.2768 kcal/mol@LB@Unfolding Energy - mRNA 3.69768 kcal/mol@LB@Unfolding Energy - sRNA 6.213 kcal/mol@LB@@LB@Position - mRNA 17 -- 34@LB@Position - sRNA 51 -- 73@LB@Position Seed - mRNA 28 -- 34@LB@Position Seed - sRNA 51 -- 57@LB@
4	8.02e-06	0.007054	b0425	panE	-14.83	0.000836	22 -- 49	1 -- 32	2-dehydropantoate reductase NADPH-specific	_____________21________________________________50\n_____________\|_________________________________\|\n5'-AUC...AUAUC_________________UU____________U_AUUUU...CGC-3'\n______________GAAAGAUGG__CAUCUU__CCUCU___CCCU_C\n______________\|\|\|\|\|\|\|:\|__\|\|\|\|\|\|__\|\|\|\|\|___\|\|\|\|_\|\n______________CUUUCUAUC__GUAGAA__GGAGA___GGGA_G\n3'-AUU...CCAGA_________UU______U______CAU____U_-5'\n_____________\|________________________________\|\n_____________33_______________________________1\n	24 -- 30	24 -- 30	-28.6113 kcal/mol	4.98037 kcal/mol	8.82471 kcal/mol	21 50@LB@ \| \|@LB@5'-AUC...AUAUC UU U AUUUU...CGC-3'@LB@ GAAAGAUGG CAUCUU CCUCU CCCU C@LB@ \|\|\|\|\|\|\|:\| \|\|\|\|\|\| \|\|\|\|\| \|\|\|\| \|@LB@ CUUUCUAUC GUAGAA GGAGA GGGA G@LB@3'-AUU...CCAGA UU U CAU U -5'@LB@ \| \|@LB@ 33 1@LB@@LB@@LB@Energy -14.83 kcal/mol@LB@Hybridization Energy -28.6113 kcal/mol@LB@Unfolding Energy - mRNA 4.98037 kcal/mol@LB@Unfolding Energy - sRNA 8.82471 kcal/mol@LB@@LB@Position - mRNA 22 -- 49@LB@Position - sRNA 1 -- 32@LB@Position Seed - mRNA 24 -- 30@LB@Position Seed - sRNA 24 -- 30@LB@
114	0.003723	0.1147	b2327	yfcA	-8.38	0.125082	22 -- 29	1 -- 8	TauE/TSUP family inner membrane protein	_____________21_______30\n_____________\|________\|\n5'-CAU...UACGU________CGAUA...GUG-3'\n______________UGCCCUGC\n______________\|:\|\|\|\|:\|\n______________AUGGGAUG\n3'-AUU...GAGAC________-5'\n_____________\|_______\|\n_____________9_______1\n	23 -- 29	1 -- 7	-12.241 kcal/mol	1.76759 kcal/mol	2.11603 kcal/mol	21 30@LB@ \| \|@LB@5'-CAU...UACGU CGAUA...GUG-3'@LB@ UGCCCUGC@LB@ \|:\|\|\|\|:\|@LB@ AUGGGAUG@LB@3'-AUU...GAGAC -5'@LB@ \| \|@LB@ 9 1@LB@@LB@@LB@Energy -8.38 kcal/mol@LB@Hybridization Energy -12.241 kcal/mol@LB@Unfolding Energy - mRNA 1.76759 kcal/mol@LB@Unfolding Energy - sRNA 2.11603 kcal/mol@LB@@LB@Position - mRNA 22 -- 29@LB@Position - sRNA 1 -- 8@LB@Position Seed - mRNA 23 -- 29@LB@Position Seed - sRNA 1 -- 7@LB@
14	5.486e-05	0.01183	b0420	dxs	-9.76	0.053178	24 -- 31	1 -- 8	1-deoxyxylulose-5-phosphate synthase thiamine triphosphate-binding FAD-requiring	_____________23_______32\n_____________\|________\|\n5'-ACC...GUACC________ACUUC...ACG-3'\n______________UACCCUGC\n______________\|\|\|\|\|\|:\|\n______________AUGGGAUG\n3'-AUU...GAGAC________-5'\n_____________\|_______\|\n_____________9_______1\n	25 -- 31	1 -- 7	-13.3609 kcal/mol	1.5078 kcal/mol	2.11603 kcal/mol	23 32@LB@ \| \|@LB@5'-ACC...GUACC ACUUC...ACG-3'@LB@ UACCCUGC@LB@ \|\|\|\|\|\|:\|@LB@ AUGGGAUG@LB@3'-AUU...GAGAC -5'@LB@ \| \|@LB@ 9 1@LB@@LB@@LB@Energy -9.76 kcal/mol@LB@Hybridization Energy -13.3609 kcal/mol@LB@Unfolding Energy - mRNA 1.5078 kcal/mol@LB@Unfolding Energy - sRNA 2.11603 kcal/mol@LB@@LB@Position - mRNA 24 -- 31@LB@Position - sRNA 1 -- 8@LB@Position Seed - mRNA 25 -- 31@LB@Position Seed - sRNA 1 -- 7@LB@
61	0.0009386	0.05413	b0574	cusB	-12.39	0.007718	27 -- 84	1 -- 59	copper/silver efflux system membrane fusion protein	_____________26_____________________________________________________________85\n_____________\|______________________________________________________________\|\n5'-AAA...AUCAC______________CC_____CU__C_G____U__CCAU___C______A_________C__AGACG...AAA-3'\n______________GAUCCGAUUGC_UG__GUGAA__GG_C_GAGA_GA____GCG_UUUACC_UC___ACCC_GC\n______________:\|\|\|\|\|\|\|\|:\|_\|\|__\|\|:\|\|__\|\|_\|_\|\|:\|_\|\|____:\|:_:\|\|\|\|\|_\|\|___\|\|\|\|_:\|\n______________UUAGGCUAAUG_AC__CAUUU__CC_G_CUUU_CU____UGU_GAAUGG_AG___UGGG_UG\n3'-AUU...UCGGU___________C__UU_____U___A_A_______AUCU___A_________ACA____A__-5'\n_____________\|_____________________________________________________________\|\n_____________60____________________________________________________________1\n	31 -- 37	49 -- 55	-39.7476 kcal/mol	14.6812 kcal/mol	12.7027 kcal/mol	26 85@LB@ \| \|@LB@5'-AAA...AUCAC CC CU C G U CCAU C A C AGACG...AAA-3'@LB@ GAUCCGAUUGC UG GUGAA GG C GAGA GA GCG UUUACC UC ACCC GC@LB@ :\|\|\|\|\|\|\|\|:\| \|\| \|\|:\|\| \|\| \| \|\|:\| \|\| :\|: :\|\|\|\|\| \|\| \|\|\|\| :\|@LB@ UUAGGCUAAUG AC CAUUU CC G CUUU CU UGU GAAUGG AG UGGG UG@LB@3'-AUU...UCGGU C UU U A A AUCU A ACA A -5'@LB@ \| \|@LB@ 60 1@LB@@LB@@LB@Energy -12.39 kcal/mol@LB@Hybridization Energy -39.7476 kcal/mol@LB@Unfolding Energy - mRNA 14.6812 kcal/mol@LB@Unfolding Energy - sRNA 12.7027 kcal/mol@LB@@LB@Position - mRNA 27 -- 84@LB@Position - sRNA 1 -- 59@LB@Position Seed - mRNA 31 -- 37@LB@Position Seed - sRNA 49 -- 55@LB@
98	0.002849	0.1023	b0772	ybhC	-6.17	0.383539	27 -- 33	49 -- 55	acyl-CoA thioesterase lipoprotein	_____________26______34\n_____________\|_______\|\n5'-UCA...CGCCU_______UGCGA...AUC-3'\n______________CGAUUAC\n______________\|\|\|\|\|\|\|\n______________GCUAAUG\n3'-AUU...UUUAG_______CACUU...AUG-5'\n_____________\|_______\|\n_____________56______48\n	27 -- 33	49 -- 55	-7.86935 kcal/mol	1.39337 kcal/mol	0.311712 kcal/mol	26 34@LB@ \| \|@LB@5'-UCA...CGCCU UGCGA...AUC-3'@LB@ CGAUUAC@LB@ \|\|\|\|\|\|\|@LB@ GCUAAUG@LB@3'-AUU...UUUAG CACUU...AUG-5'@LB@ \| \|@LB@ 56 48@LB@@LB@@LB@Energy -6.17 kcal/mol@LB@Hybridization Energy -7.86935 kcal/mol@LB@Unfolding Energy - mRNA 1.39337 kcal/mol@LB@Unfolding Energy - sRNA 0.311712 kcal/mol@LB@@LB@Position - mRNA 27 -- 33@LB@Position - sRNA 49 -- 55@LB@Position Seed - mRNA 27 -- 33@LB@Position Seed - sRNA 49 -- 55@LB@

Details of Selected Interaction Download Interaction Details

mRNA

sRNA

Energy

Hybridization Energy

Unfolding Energy - mRNA

Unfolding Energy - sRNA

Position - mRNA

Position - sRNA

Position Seed - mRNA

Position Seed - sRNA

Evolutionary conservation of mRNA targets (alignment generated with Jalview)

Evolutionary conservation of sRNA (alignment generated with Jalview)

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When using CopraRNA please cite :

Patrick R. Wright, Jens Georg, Martin Mann, Dragos A. Sorescu, Andreas S. Richter, Steffen Lott, Robert Kleinkauf, Wolfgang R. Hess, and Rolf Backofen
CopraRNA and IntaRNA: predicting small RNA targets, networks and interaction domains
Nucleic Acids Research, 2014, 42 (W1), W119-W123.
Patrick R. Wright, Andreas S. Richter, Kai Papenfort, Martin Mann, Joerg Vogel, Wolfgang R. Hess, Rolf Backofen and Jens Georg
Comparative genomics boosts target prediction for bacterial small RNAs
Proc Natl Acad Sci USA, 2013, 110 (37), E3487-E3496.
Martin Raden, Syed M Ali, Omer S Alkhnbashi, Anke Busch, Fabrizio Costa, Jason A Davis, Florian Eggenhofer, Rick Gelhausen, Jens Georg, Steffen Heyne, Michael Hiller, Kousik Kundu, Robert Kleinkauf, Steffen C Lott, Mostafa M Mohamed, Alexander Mattheis, Milad Miladi, Andreas S Richter, Sebastian Will, Joachim Wolff, Patrick R Wright, and Rolf Backofen
Freiburg RNA tools: a central online resource for RNA-focused research and teaching
Nucleic Acids Research, 46(W1), W25-W29, 2018.

Results are computed with CopraRNA version 2.1.2

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